signifinder
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see signifinder.
Implementations of transcriptional cancer signatures
Bioconductor version: 3.18
signifinder is an R package for computing and exploring a compendium of tumor signatures. It allows to compute a variety of signatures, based on gene expression values, and return single-sample scores. Currently, signifinder contains 46 distinct signatures collected from the literature, relating to multiple tumors and multiple cancer processes.
Author: Stefania Pirrotta [cre, aut] 
, Enrica Calura [aut]
Maintainer: Stefania Pirrotta <stefania.pirrotta at phd.unipd.it>
citation("signifinder")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("signifinder")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("signifinder")| signifinder vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, GeneExpression, GeneTarget, ImmunoOncology, Microarray, RNASeq, ReportWriting, SingleCell, Software, Spatial, Visualization |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (1.5 years) |
| License | AGPL-3 |
| Depends | R (>= 4.3.0) |
| Imports | ggplot2, org.Hs.eg.db, patchwork, AnnotationDbi, BiocGenerics, ComplexHeatmap, cowplot, DGEobj.utils, GSVA, IRanges, SummarizedExperiment, consensusOV, dplyr, ensembldb, ggridges, grid, magrittr, matrixStats, maxstat, methods, openair, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, stats, survival, survminer, viridis, SpatialExperiment |
| System Requirements | |
| URL | https://github.com/CaluraLab/signifinder |
| Bug Reports | https://github.com/CaluraLab/signifinder/issues |
See More
| Suggests | BiocStyle, knitr, kableExtra, testthat (>= 3.0.0), edgeR, limma |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | signifinder_1.4.0.tar.gz |
| Windows Binary | signifinder_1.4.0.zip |
| macOS Binary (x86_64) | signifinder_1.4.0.tgz |
| macOS Binary (arm64) | signifinder_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/signifinder |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/signifinder |
| Bioc Package Browser | https://code.bioconductor.org/browse/signifinder/ |
| Package Short Url | https://bioconductor.org/packages/signifinder/ |
| Package Downloads Report | Download Stats |